Up to 22 pesticides could be lost to European farmers, following agreement on a new law between the European Council and the European Parliament late on 17 December.

The French presidency of the EU and the Parliament reached a deal last night following months of wrangling over plans to revise legislation dating from 1991. The proposed rule changes had roused strong opposition from the pesticides industry and from some member states – notably the UK. To become law, the agreement must be formally endorsed by ministers and by a vote of the European Parliament in full plenary session, but MEPs are not expected to pose a major challenge.

Hiltrud Breyer, the German Green MEP who led negotiations on behalf of the European Parliament, said in a statement that the agreement was “a milestone for the environment, health and consumer protection in Europe. The EU will set a global precedent by phasing out highly toxic pesticides.”

Breyer’s officials say that 22 pesticides – fungicides and insecticides – could be gradually phased out of use in European markets. Negotiators agreed to ban some substances that damage human health by mimicking or disturbing hormones (endocrine disruptors). Under the agreement, a pesticide is deemed to be an endocrine disruptor if it affects reproduction, causes or contributes to cancer or poses a significant risk to human health. Breyer’s officials say that fewer than 5% of pesticides currently on the market could be withdrawn.

But the Parliament failed to win a complete ban on endocrine disruptors. If a pesticide is deemed to combat a serious danger to plant health, it can be approved for use even if it does not meet the safety criteria. This exception will not be a catch-all exclusion for all countries, but only for the country that succeeds in proving its case.

Euros Jones, the director of regulatory affairs at the European Crop Protection Agency (ECPA), condemned the decision on endocrine disruptors as “scientific rubbish”. He said that the negotiators were “re-inventing science” because they were not following scientifically accepted definitions of endocrine disruptors.

“The key point is that these [pesticides] have already been evaluated in the stringent evaluation system that we have in the EU and this is a very exhaustive regulatory process,” Jones said.

ECPA will ask the European Parliament to vote separately on the endocrine disruptors amendments when MEPs vote in January.

Negotiators also agreed that the EU should be split into three zones (north, central and south). If a product is recognised in one country, it will be recognised in all countries within its zone. However the Parliament won an exemption that enables individual countries to ban a product if they have environmental worries.

As well as this regulation, the EU also finalised a directive on pesticides that will call on member states to draw up action plans, with targets and timetables, “to reduce risks and impacts of pesticide use on health and the environment”.

But the Council threw out a proposal by the Parliament to ban 50% of chemicals currently deemed to be “of high concern” or “very toxic”. This was “absolutely no-go for the Council” said one source familiar with the negotiations.